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Principal Investigator: YURIJ IONOV
Organization: UNIVERSITY OF CONNECTICUT SCH OF MED/DNT
Fiscal Year: 2021
Award: $466,702
Funding agency: National Cancer Institute
PROJECT SUMMARY/ABSTRACT
We propose to create a library of chemotherapy-induced cancer neoepitopes (chemo-neoepitopes) that
are shared between breast cancers, do not have to be customized for each tumor, and can be used for
immunotherapy of any cancers with mutated p53. This approach is based on the following principles:
i. Cells experiencing DNA damage repress transcription of several cell cycle genes [1-3]
ii. Cells with mutated p53 genes are unable to mediate this transcriptional repression in response
to DNA damage, creating a clear transcriptional difference between normal and cancer cells
within hosts undergoing DNA-damaging chemotherapies [1-3]
iii. Certain chemotherapies (e.g., platinums, 5 Fluorouracil, etc.), in addition to causing DNA
damage, cause abnormal splicing leading to generation of abnormal transcripts that are recurrent
and reproducible in cells treated with such chemotherapy [4-12]
iv. The abnormal splicing products undergo Nonsense Mediated mRNA Decay, but not before a
Pioneer Round of translation [13-15], which is known to create antigenic epitopes [16-20].
Based on these principles and our preliminary data we posit that:
Selected chemotherapies lead to generation of products of abnormal splicing (Chemotherapy-
induced Products of Abnormal Splicing or CiPAS) that are not expressed in untreated cells or
in treated cells with a functional p53, and
CiPAS create new and predictable neoepitopes or chemo-neoepitopes, immunization with which,
before chemotherapy will lead to tumor immunity that will contribute to tumor eradiation.
Aim 1. To identify CiPAS which are recurrently expressed during chemotherapy in breast tumors
that harbor p53 mutations. We will use bulk RNA-Seq to identify, and both bulk and single cell RT-
PCR to validate CiPAS specifically and recurrently expressed in p53-/- breast tumors.
Aim 2. To test the hypothesis that CiPAS generate cancer-specific chemo-neoepitopes that can
elicit immune protection from tumor growth:
a. Identify chemo-neoepitopes generated from CiPAS in chemotherapy-treated mouse tumors by
using RNA-Seq, mass-spectrometry and an integrative bioinformatics approach.
b. Test chemo-neoepitopes for their ability to elicit CD8 and CD4 T cells and tumor rejectionusing
the triple negative 4T1 breast cancer tumor line in syngeneic mice.
Altogether, these studies will establish the identity of mouse and human CiPAS, and will set the stage
for testing of immunogenicity and anti-tumor activity of CiPAS in cancer patients.
Terms: <21+ years old><4T1><5-FU><5-Fluracil><5FU><Adult><Adult Human><Antigenic Determinants><Antimorphic mutation><Antineoplastic Vaccine><Antioncogene Protein p53><BA2R><Binding Determinants><Bio-Informatics><Bioinformatics><Body Tissues><Breast Cancer><Breast Neoplasms><Breast Tumors><CBDCA><CCG1><CD4 Cells><CD4 Positive T Lymphocytes><CD4 T cells><CD4 helper T cell><CD4 lymphocyte><CD4+ T-Lymphocyte><CD4-Positive Lymphocytes><CD8><CD8B><CD8B1><CD8B1 gene><Cancer Patient><Cancer Vaccines><Cancers><Carboplatin><Carboplatino><Cell Body><Cell Cycle Gene 1><Cells><Cellular Tumor Antigen P53><Custom><DNA Damage><DNA Injury><Data><Dominant Negative><Dominant-Negative Mutant><Dominant-Negative Mutation><Epitopes><Fluoro Uracil><Fluorouracil><Fluoruracil><Fluouracil><Gene Down-Regulation><Gene Transcription><Generations><Genetic Alteration><Genetic Change><Genetic Transcription><Genetic defect><Human><Human Cell Line><Immune><Immune mediated therapy><Immunes><Immunization><Immunologic Sensitization><Immunologic Stimulation><Immunological Sensitization><Immunological Stimulation><Immunologically Directed Therapy><Immunostimulation><Immunotherapy><LYT3><Lead><Libraries><MCF-10A><MCF10A><MCF10A cells><MDA MB 231><MDA-231><MDA-MB231><Malignant Cell><Malignant Neoplasms><Malignant Tumor><Mammary Cancer><Mammary Neoplasms><Mass Photometry/Spectrum Analysis><Mass Spectrometry><Mass Spectroscopy><Mass Spectrum><Mass Spectrum Analyses><Mass Spectrum Analysis><Mediating><Mice><Mice Mammals><Modern Man><Mouse Cell Line><Murine><Mus><Mutate><Mutation><Neoplasm Vaccines><Normal Cell><Oncoprotein p53><P53><Patients><Pb element><Phosphoprotein P53><Phosphoprotein pp53><Platinum><Platinum Black><Protein TP53><Pt element><RNA Expression><RNA Seq><RNA Splicing><RNA sequencing><RNAseq><RT-PCR><RTPCR><Recurrence><Recurrent><Reproducibility><Reverse Transcriptase Polymerase Chain Reaction><Solid><Splicing><T4 Cells><T4 Lymphocytes><TAF1><TAF1 RNA Polymerase II TATA Box Binding Protein-Associated Factor 250-kD><TAF1 gene><TAF2A><TAFII250><TATA Box-Binding Protein-Associated Factor 2A><TBP-Associated Factor RNA Polymerase II 250-kD><TFIID><TNBC><TP53><TP53 gene><TRP53><Testing><Tissues><Transcript><Transcription><Transcription Repression><Transcriptional Repression><Transfection><Translations><Tumor Immunity><Tumor Protein p53><Tumor Protein p53 Gene><Tumor Vaccines><adulthood><anti-tumor immunity><anti-tumor vaccine><antitumor immunity><antitumor vaccine><base><cancer cell><cancer immunity><cancer recurrence><chemotherapy><differential expression><differentially expressed><experience><gene repression><genome mutation><heavy metal Pb><heavy metal lead><immune therapeutic approach><immune therapeutic interventions><immune therapeutic regimens><immune therapeutic strategy><immune therapy><immune-based therapies><immune-based treatments><immuno therapy><immunogenicity><mRNA Decay><malignancy><malignant breast neoplasm><malignant breast tumor><mammary tumor><mouse model><murine model><neo-antigen><neo-epitopes><neoantigens><neoepitopes><neoplasm/cancer><novel><p53 Antigen><p53 Genes><p53 Tumor Suppressor><prevent><preventing><protein p53><response><reverse transcriptase PCR><transcriptional differences><transcriptome sequencing><triple-negative breast cancer><triple-negative invasive breast carcinoma><tumor><tumor growth><vaccine for cancer>